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@metagenomics Computational Metagenomics

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    21 repositories

    • metagenomics-tk

      Public
      The Metagenomics-Toolkit is a scalable, data agnostic workflow that automates the analysis of short and long metagenomic reads obtained from Illumina or Oxford Nanopore Technology devices, respectively.
      workflowbioinformaticsnanoporenextflowmetagenomicsillumina
      Nextflow
      •
      GNU Affero General Public License v3.0
      •3•18•46•37•Updated Oct 15, 2025Oct 15, 2025

    • submg

      Public
      ENA metagenome upload
      Python
      •
      MIT License
      •1•6•0•0•Updated Jul 18, 2025Jul 18, 2025

    • long-read-training

      Public
      Long Read Training Course
      12•0•0•0•Updated Jul 9, 2025Jul 9, 2025

    • wastewater-study

      Public
      R
      •0•0•0•0•Updated Jul 2, 2025Jul 2, 2025

    • denbi-nanopore-training

      Public
      de.NBI Nanopore Training Course
      12•20•0•4•Updated Jun 13, 2025Jun 13, 2025

    • prokka

      Public
      ⚡ ♒ Rapid prokaryotic genome annotation
      Perl
      •231•0•0•0•Updated May 5, 2025May 5, 2025

    • metagenomics-workshop

      Public
      16•8•1•1•Updated Mar 11, 2025Mar 11, 2025

    • 2015-biogas-cebitec

      Public
      Bremges et al. (2015). GigaScience, 4:33.
      TeX
      •
      MIT License
      •6•12•0•0•Updated Dec 29, 2023Dec 29, 2023

    • primer-schemes

      Public
      Primer schemes for real-time genome epidemiology
      Python
      •
      Creative Commons Attribution 4.0 International
      •42•0•0•0•Updated Feb 22, 2021Feb 22, 2021

    • NanoporeRealTimeAnalysis

      Public
      Java
      •1•0•0•0•Updated Jul 25, 2020Jul 25, 2020

    • MeRaGENE

      Public
      Python
      •
      MIT License
      •2•4•23•0•Updated Aug 24, 2018Aug 24, 2018

    • gru

      Public
      Pipeline for evaluation of 2d Nanopore reads
      HTML
      •0•0•1•0•Updated Oct 24, 2017Oct 24, 2017

    • cloudcomputing

      Public
      0•0•0•0•Updated Jun 16, 2016Jun 16, 2016

    • ncbi-genome-download

      Public
      Scripts to download genomes from the NCBI FTP servers
      Python
      •
      Apache License 2.0
      •179•1•0•0•Updated May 27, 2016May 27, 2016

    • MeCorS

      Public
      Metagenome-enabled error correction of single cell sequencing reads
      C
      •
      MIT License
      •2•0•0•0•Updated Mar 24, 2016Mar 24, 2016

    • pyani

      Public
      Python module for average nucleotide identity analyses
      Python
      •
      MIT License
      •56•0•0•0•Updated Mar 18, 2016Mar 18, 2016

    • PyFlows

      Public
      Generic python workflows, optimized for parallel environments (local server and/or SGE computing cluster)
      Python
      •
      MIT License
      •2•0•0•0•Updated Feb 24, 2016Feb 24, 2016

    • Mesos

      Public
      Mesos Scheduler Implementations
      Java
      •1•0•2•0•Updated Feb 10, 2016Feb 10, 2016

    • EG_MinION_2016

      Public
      Edinburgh Genomics MinION training 2016
      13•0•0•0•Updated Feb 3, 2016Feb 3, 2016

    • scripts

      Public
      Miscellaneous scripts
      Python
      •
      MIT License
      •19•1•0•0•Updated Nov 4, 2015Nov 4, 2015

    • sc

      Public
      C
      •1•0•0•0•Updated Dec 19, 2014Dec 19, 2014